Iterates through the tree array and creates phylonodes in Chado.

The function iterates through the tree in a top-down approach adding parent internal nodes prior to leaf nodes. Each node of the tree should have the following fields:

-name: The name (or label) for this node. -depth: The depth of the node in the tree. -is_root: Set to 1 if this node is a root node. -is_leaf: Set to 1 if this node is a leaf node. -is_internal: Set to 1 if this node is an internal node. -left_index: The index of the node to the left in the tree. -right_index: The index of the node to the right in the tree. -branch_set: An array containing a list of nodes of that are children of the node. -parent: The name of the parent node. -organism_id: The organism_id for associtating the node with an organism. -properties: An array of key/value pairs where the key is the cvterm_id and the value is the property value. These properties will be assocaited with the phylonode.

Prior to importing the tree the indicies can be set by using the tripal_phylogeny_assign_tree_indices() function.

Parameters

$tree: The tree array.

$options: The options provide some direction for how the tree is imported. The following keys can be used: -taxonomy: Set to 1 if this tree is a taxonomic tree. Set to 0 otherwise. -leaf_type: Set to the leaf type name. If this is a non-taxonomic tree that is associated with features, then this should be the Sequence Ontology term for the feature (e.g. polypeptide). If this is a taxonomic tree then this option is not needed. -match: Set to either 'name' or 'uniquename'. This is used for matching the feature name or uniquename with the node name. This is not needed for taxonomic trees. -match_re: Set to a regular that can be used for matching the node name with the feature name if the node name is not identical to the feature name.

$vocab: Optional. An array containing a set of key/value pairs that maps node types to CV terms. The keys must be 'root', 'internal' or 'leaf'. If no vocab is provded then the terms provided by the tripal_phylogeny CV will be used.

$parent: This argument is not needed when the funtion is first called. This function is recursive and this argument is used on recursive calls.

File

tripal_phylogeny/includes/tripal_phylogeny.import_tree.inc, line 215

Code

function tripal_phylogeny_import_tree(&$tree, $phylotree, $options, $vocab = array(), $parent = NULL) {

  // Get the vocabulary terms used to describe nodes in the tree if one
  // wasn't provided.
  if (count($vocab) == 0) {
    $vocab = tripal_phylogeny_get_node_types_vocab();
  }

  if (is_array($tree) and array_key_exists('name', $tree)) {
    $values = array(
      'phylotree_id' => $phylotree->phylotree_id,
      'left_idx' => $tree['left_index'],
      'right_idx' => $tree['right_index'],
    );
    // Add in any optional values to the $values array if they are present
    if (!empty($tree['name']) and $tree['name'] != '') {
      $values['label'] = $tree['name'];
    }
    if (!empty($tree['length']) and $tree['length'] != '') {
      $values['distance'] = $tree['length'];
    }
    // Set the type of node
    if ($tree['is_root']) {
      $values['type_id'] = $vocab['root']->cvterm_id;
    }
    else if ($tree['is_internal']) {
      $values['type_id'] = $vocab['internal']->cvterm_id;
      $values['parent_phylonode_id'] = $parent['phylonode_id'];
      // TOOD: a feature may be associated here but it is recommended that it
      // be a feature of type SO:match and should represent the alignment of
      // all features beneath it.
    }
    else if ($tree['is_leaf']) {
      $values['type_id'] = $vocab['leaf']->cvterm_id;
      $values['parent_phylonode_id'] = $parent['phylonode_id'];

      // Match this leaf node with an organism or feature depending on the
      // type of tree. But we can't do that if we don't have a name.
      if (!empty($tree['name']) and $tree['name'] != '') {
        if (!$options['taxonomy']) {

          // This is a sequence-based tree. Try to match leaf nodes with features.
          // First, Get the Name and uniquename for the feature
          $matches = array();
          $sel_values = array();
          if ($options['match'] == "name") {
            $sel_values['name'] = $tree['name'];
            $re = $options['name_re'];
            if (preg_match("/$re/", $tree['name'], $matches)) {
              $sel_values['name'] = $matches[1];
            }
          }
          else {
            $sel_values['uniquename'] = $tree['name'];
            $re = $options['name_re'];
            if (preg_match("/$re/", $tree['name'], $matches)) {
              $sel_values['uniquename'] = $matches[1];
            }
          }
          $sel_values['type_id'] = array(
            'name' => $options['leaf_type'],
            'cv_id' => array(
              'name' => 'sequence'
            ),
          );
          $sel_columns = array('feature_id');
          $feature = chado_select_record('feature', $sel_columns, $sel_values);
          if (count($feature) > 1) {
            // Found multiple features, cannot make an association.
          }
          else if (count($feature) == 1) {
            $values['feature_id'] = $feature[0]->feature_id;
          }
          else {
            // Could not find a feature that matches the name or uniquename
          }
        }
      }
    }

    // Insert the new node and then add it's assigned phylonode_id to the node
    $phylonode = chado_insert_record('phylonode', $values);
    $tree['phylonode_id'] = $phylonode['phylonode_id'];

    // This is a taxonomic tree, so assocaite this node with an
    // organism if one is provided.
    if (array_key_exists('organism_id', $tree)) {
      $values = array(
        'phylonode_id' => $tree['phylonode_id'],
        'organism_id' => $tree['organism_id']
      );
      $pylonode_organism = chado_insert_record('phylonode_organism', $values);
    }

    // Associate any properties
    if (array_key_exists('properties', $tree)) {
      foreach ($tree['properties'] as $type_id => $value) {
        $values = array(
          'phylonode_id' => $tree['phylonode_id'],
          'type_id' => $type_id,
          'value' => $value,
        );
        $pylonode_organism = chado_insert_record('phylonodeprop', $values);
      }
    }
  }
  if (is_array($tree) and array_key_exists('branch_set', $tree)) {
    foreach ($tree['branch_set'] as $key => $node) {
      tripal_phylogeny_import_tree($tree['branch_set'][$key], $phylotree, $options, $vocab, $tree);
    }
  }
}